From 719c9febac2eaff9483fda487b57684afbb59bb2 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 05 Mar 2014 16:47:50 +0000
Subject: [PATCH] dont know
---
src/io.c | 586 +++++++++++++++++++++++++++++++++++++++++++++++++++------
1 files changed, 518 insertions(+), 68 deletions(-)
diff --git a/src/io.c b/src/io.c
index 064155c..b2659db 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1,29 +1,357 @@
-#include<general.h>
+#include "general.h"
#include<stdio.h>
#include "io.h"
-#include "confuse.h"
+#include <confuse.h>
+#include "vertex.h"
+#include "bond.h"
#include<string.h>
+#include<stdlib.h>
#include <sys/types.h>
#include <dirent.h>
+#include "initial_distribution.h"
+#include "poly.h"
+
+
+
+/** DUMP STATE TO DISK DRIVE **/
+
+ts_bool dump_state(ts_vesicle *vesicle){
+
+ /* save current state with wrong pointers. Will fix that later */
+ ts_uint i,j,k;
+ ts_ulong off;
+ FILE *fh=fopen("dump.bin","wb");
+
+ /* dump vesicle */
+ fwrite(vesicle, sizeof(vesicle),1,fh);
+ /* dump vertex list */
+ fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
+ /* dump bond list */
+ fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
+ /* dump triangle list */
+ fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
+ /* dump cell list */
+ fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
+ /* dump poly list */
+ fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
+ /* level 1 complete */
+
+ /*dump vertices*/
+ for(i=0;i<vesicle->vlist->n;i++){
+ fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
+ /* dump pointer offsets for:
+ neigh
+ bond
+ tria
+ cell is ignored
+ */
+ for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
+ off=(ts_ulong)(vesicle->vlist->vtx[i]->neigh[j]-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+ for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
+ off=(ts_ulong)(vesicle->vlist->vtx[i]->bond[j]-vesicle->blist->bond[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+ for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
+ off=(ts_ulong)(vesicle->vlist->vtx[i]->tristar[j]-vesicle->tlist->tria[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+// off=(ts_ulong)(vesicle->vlist->vtx[i]->cell-vesicle->clist->cell[0]);
+// fwrite(&off,sizeof(ts_ulong),1,fh);
+
+ }
+
+ /*dump bonds*/
+ for(i=0;i<vesicle->blist->n;i++){
+ fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
+ /* dump pointer offsets for vtx1 and vtx2 */
+ off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+
+ /*dump triangles*/
+ for(i=0;i<vesicle->tlist->n;i++){
+ fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
+ /* dump pointer offsets for vertex */
+ off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[0]-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[1]-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[2]-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ /* dump pointer offsets for neigh */
+ for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
+ off=(ts_ulong)(vesicle->tlist->tria[i]->neigh[j]-vesicle->tlist->tria[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+ }
+
+ /*dump cells and its contents is not dumped but recalculated on restore*/
+
+/* for(i=0;i<vesicle->clist->cellno;i++){
+ fwrite(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
+ for(j=0;j<vesicle->clist->cell[i]->nvertex;j++){
+ off=(ts_ulong)(vesicle->clist->cell[i]->vertex[j]-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+ }
+*/
+
+
+ /*dump polymeres */
+ for(i=0;i<vesicle->poly_list->n;i++){
+ fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
+ }
+
+ /* dump poly vertex(monomer) list*/
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+ /* dump offset for neigh and bond */
+ for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
+ off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+ for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
+ off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+ }
+ }
+ /* dump poly bonds between monomers list*/
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
+ fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
+ /* dump vtx1 and vtx2 offsets */
+ off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+ }
+
+/* pointer offsets for fixing the restored pointers */
+/* need pointers for
+ vlist->vtx
+ blist->bond
+ tlist->tria
+ clist->cell
+ poly_list->poly
+ and for each poly:
+ poly_list->poly->vtx
+ poly_list->poly->bond
+*/
+
+ fwrite(vesicle->vlist->vtx, sizeof(ts_vertex *),1,fh);
+ fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
+ fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
+ fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
+ fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
+ for(i=0;i<vesicle->poly_list->n;i++){
+ fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
+ fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),1,fh);
+ }
+ fclose(fh);
+ return TS_SUCCESS;
+}
+
+
+/** RESTORE DUMP FROM DISK **/
+ts_vesicle *restore_state(){
+ ts_uint i,j,k;
+ FILE *fh=fopen("dump.bin","rb");
+ ts_uint retval;
+ ts_ulong off;
+
+/* we restore all the data from the dump */
+ /* restore vesicle */
+ ts_vesicle *vesicle=(ts_vesicle *)calloc(1,sizeof(ts_vesicle));
+ retval=fread(vesicle, sizeof(vesicle),1,fh);
+ /* restore vertex list */
+ vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
+ retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
+ /* restore bond list */
+ vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
+ retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
+ /* restore triangle list */
+ vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
+ retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
+ /* restore cell list */
+ vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
+ retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
+ /* restore poly list */
+ vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
+ retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
+ /* level 1 complete */
+
+ /*restore vertices*/
+ vesicle->vlist->vtx=(ts_vertex **)calloc(vesicle->vlist->n,sizeof(ts_vertex *));
+ for(i=0;i<vesicle->vlist->n;i++){
+ vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
+ /*restore neigh, bond, tristar. Ignoring cell */
+ vesicle->vlist->vtx[i]->neigh=(ts_vertex **)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex *));
+ for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[0]+off;
+ }
+ vesicle->vlist->vtx[i]->bond=(ts_bond **)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond *));
+ for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[0]+off;
+ }
+
+ vesicle->vlist->vtx[i]->tristar=(ts_triangle **)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle *));
+ for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[0]+off;
+ }
+
+ }
+
+ /*restore bonds*/
+ vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *));
+ for(i=0;i<vesicle->blist->n;i++){
+ vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
+ retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
+ /* restore vtx1 and vtx2 */
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[0]+off;
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[0]+off;
+ }
+
+ /*restore triangles*/
+ vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *));
+ for(i=0;i<vesicle->tlist->n;i++){
+ vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
+ retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
+ /* restore pointers for vertices */
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[0]+off;
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[0]+off;
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[0]+off;
+ /* restore pointers for neigh */
+ for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[0]+off;
+ }
+
+ }
+
+ /*restore cells */
+/*TODO: do we need to recalculate cells here? */
+/* vesicle->clist->cell=(ts_cell **)malloc(vesicle->clist->cellno*sizeof(ts_cell *));
+ for(i=0;i<vesicle->clist->cellno;i++){
+ vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
+ retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
+ }
+*/
+ /*restore polymeres */
+ vesicle->poly_list->poly = (ts_poly **)calloc(vesicle->poly_list->n,sizeof(ts_poly *));
+ for(i=0;i<vesicle->poly_list->n;i++){
+ vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
+ retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
+ }
+
+ /* restore poly vertex(monomer) list*/
+ for(i=0;i<vesicle->poly_list->n;i++){
+ vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+
+ /* restore neigh and bonds */
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
+ for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
+ }
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
+ for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[0]+off;
+ }
+
+ }
+ }
+ /* restore poly bonds between monomers list*/
+ for(i=0;i<vesicle->poly_list->n;i++){
+ vesicle->poly_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond *));
+ for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
+ vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
+ /* restore vtx1 and vtx2 */
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
+ }
+ }
+
+
+ /* recalculate pointers using saved information on pointer addresses */
+ /* following pointers need to be recalculated:
+ all vtx->neigh
+ all vtx->tristar
+ all vtx->bond
+ vtx->cell
+ vtx->grafted_poly
+ bond->vtx1
+ bond->vtx2
+ tria->vertex[*]
+ tria->neigh
+ cell->vertex
+ poly->grafted_vtx
+ poly->vlist->vtx->neigh
+ poly->vlist->vtx->bond
+ poly->vlist->vtx->cell
+ */
+
+ /* read pointers from disk */
+/* fwrite(vesicle->vlist->vtx, sizeof(ts_vertex *),1,fh);
+ fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
+ fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
+ fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
+ fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
+ for(i=0;i<vesicle->poly_list->n;i++){
+ fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
+ fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),1,fh);
+ }
+*/
+
+
+ if(retval);
+ fclose(fh);
+ return vesicle;
+}
+
ts_bool print_vertex_list(ts_vertex_list *vlist){
ts_uint i;
printf("Number of vertices: %u\n",vlist->n);
for(i=0;i<vlist->n;i++){
- printf("%u: %f %f %f\n", vlist->vertex[i].idx,vlist->vertex[i].x, vlist->vertex[i].y, vlist->vertex[i].z);
+ printf("%u: %f %f %f\n",
+vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
}
return TS_SUCCESS;
}
ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
ts_uint i,j;
- ts_vertex *vtx=vlist->vertex;
+ ts_vertex **vtx=vlist->vtx;
printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
for(i=0;i<vlist->n;i++){
- printf("%u(%u): ",vtx[i].idx,vtx[i].neigh_no);
- for(j=0;j<vtx[i].neigh_no;j++){
- printf("(%f,%f,%f)",vtx[i].neigh[j]->x, vtx[i].neigh[j]->y,vtx[i].neigh[j]->z);
+ printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh->n);
+ for(j=0;j<vtx[i]->neigh->n;j++){
+ printf("(%f,%f,%f)",vtx[i]->neigh->vtx[j]->x,
+vtx[i]->neigh->vtx[j]->y,vtx[i]->neigh->vtx[j]->z);
}
printf("\n");
}
@@ -32,7 +360,7 @@
}
ts_bool write_vertex_fcompat_file(ts_vertex_list *vlist,ts_char *filename){
- ts_vertex *vtx=vlist->vertex;
+ ts_vertex **vtx=vlist->vtx;
ts_uint i;
FILE *fh;
@@ -42,7 +370,7 @@
return TS_FAIL;
}
for(i=0;i<vlist->n;i++)
- fprintf(fh," %E\t%E\t%E\n",vtx[i].x,vtx[i].y, vtx[i].z);
+ fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
fclose(fh);
return TS_SUCCESS;
@@ -52,10 +380,12 @@
ts_bool fprint_vertex_list(FILE *fh,ts_vertex_list *vlist){
ts_uint i,j;
for(i=0;i<vlist->n;i++){
- fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vertex[i].x,
- vlist->vertex[i].y, vlist->vertex[i].z, vlist->vertex[i].neigh_no);
- for(j=0;j<vlist->vertex[i].neigh_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vlist->vertex[i].neigh[j]-vlist->vertex+1));
+ fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
+ vlist->vtx[i]->y, vlist->vtx[i]->z,
+ vlist->vtx[i]->neigh->n);
+ for(j=0;j<vlist->vtx[i]->neigh->n;j++){
+ fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh->vtx[j]->idx));
+ //-vlist->vtx+1));
}
fprintf(fh,"\n");
}
@@ -64,10 +394,10 @@
ts_bool fprint_tristar(FILE *fh, ts_vesicle *vesicle){
ts_uint i,j;
- for(i=0;i<vesicle->vlist.n;i++){
- fprintf(fh,"\t%u",vesicle->vlist.vertex[i].tristar_no);
- for(j=0;j<vesicle->vlist.vertex[i].tristar_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist.vertex[i].tristar[j]-vesicle->tlist.triangle+1));
+ for(i=0;i<vesicle->vlist->n;i++){
+ fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
+ for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
+ fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
}
fprintf(fh,"\n");
}
@@ -75,20 +405,20 @@
}
ts_bool fprint_triangle_list(FILE *fh, ts_vesicle *vesicle){
- ts_triangle_list *tlist=&vesicle->tlist;
+ ts_triangle_list *tlist=vesicle->tlist;
ts_uint i,j;
for(i=0;i<tlist->n;i++){
- fprintf(fh,"\t%u",tlist->triangle[i].neigh_no);
- for(j=0;j<tlist->triangle[i].neigh_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(tlist->triangle[i].neigh[j]-tlist->triangle+1));
+ fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
+ for(j=0;j<tlist->tria[i]->neigh_no;j++){
+ fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
}
fprintf(fh,"\n");
for(j=0;j<3;j++){
- fprintf(fh,"\t%u",(ts_uint)(tlist->triangle[i].vertex[j]-vesicle->vlist.vertex+1));
+ fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
}
fprintf(fh,"\n");
- fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->triangle[i].xnorm,
-tlist->triangle[i].ynorm,tlist->triangle[i].znorm);
+ fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
+tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
}
return TS_SUCCESS;
@@ -98,14 +428,14 @@
ts_uint i,j;
for(i=0;i<vlist->n;i++){
fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
- vlist->vertex[i].xk,vlist->vertex[i].c,vlist->vertex[i].energy,
- vlist->vertex[i].energy_h, vlist->vertex[i].curvature, 0);
- for(j=0;j<vlist->vertex[i].neigh_no;j++){
- fprintf(fh," %.17E", vlist->vertex[i].bond_length_dual[j]);
+ vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
+ vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
+ for(j=0;j<vlist->vtx[i]->neigh->n;j++){
+ fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
}
fprintf(fh,"\n");
- for(j=0;j<vlist->vertex[i].neigh_no;j++){
- fprintf(fh," %.17E", vlist->vertex[i].bond_length[j]);
+ for(j=0;j<vlist->vtx[i]->neigh->n;j++){
+ fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
}
fprintf(fh,"\n");
}
@@ -114,8 +444,11 @@
ts_bool fprint_bonds(FILE *fh,ts_vesicle *vesicle){
ts_uint i;
- for(i=0;i<vesicle->blist.n;i++){
- fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist.bond[i].vtx1-vesicle->vlist.vertex+1),(ts_uint)(vesicle->blist.bond[i].vtx2-vesicle->vlist.vertex+1));
+ for(i=0;i<vesicle->blist->n;i++){
+ fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
+//-vesicle->vlist->vtx+1),
+ (ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
+ //-vesicle->vlist.vtx+1));
}
return TS_SUCCESS;
}
@@ -123,17 +456,16 @@
ts_bool write_dout_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
FILE *fh;
- ts_uint i,j;
fh=fopen(filename, "w");
if(fh==NULL){
err("Cannot open file %s for writing");
return TS_FAIL;
}
fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
- fprint_vertex_list(fh,&vesicle->vlist);
+ fprint_vertex_list(fh,vesicle->vlist);
fprint_tristar(fh,vesicle);
fprint_triangle_list(fh,vesicle);
- fprint_vertex_data(fh,&vesicle->vlist);
+ fprint_vertex_data(fh,vesicle->vlist);
fprint_bonds(fh,vesicle);
fclose(fh);
return TS_SUCCESS;
@@ -147,7 +479,7 @@
err("Cannot open file for reading... Nonexistant file?");
return TS_FAIL;
}
- ts_uint retval;
+ ts_uint retval=1;
while(retval!=EOF){
retval=fscanf(fh,"%s",line);
@@ -181,22 +513,23 @@
j=rindex(ent->d_name,'_');
if(j==NULL) continue;
number=strndup(j+1,j-i);
- fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atol(number),ent->d_name);
+ fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
tstep++;
free(number);
}
}
}
+ free(dir);
fprintf(fh,"</Collection>\n</VTKFile>\n");
fclose(fh);
return TS_SUCCESS;
}
ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
- ts_vertex_list *vlist=&vesicle->vlist;
- ts_bond_list *blist=&vesicle->blist;
- ts_vertex *vtx=vlist->vertex;
- ts_uint i,j;
+ ts_vertex_list *vlist=vesicle->vlist;
+ ts_bond_list *blist=vesicle->blist;
+ ts_vertex **vtx=vlist->vtx;
+ ts_uint i,j;
char filename[255];
FILE *fh;
@@ -207,29 +540,69 @@
return TS_FAIL;
}
/* Here comes header of the file */
+
+ //find number of extra vtxs and bonds of polymeres
+ ts_uint monono=0, polyno=0;
+ ts_bool poly=0;
+ if(vesicle->poly_list!=NULL){
+ if(vesicle->poly_list->poly[0]!=NULL){
+ polyno=vesicle->poly_list->n;
+ monono=vesicle->poly_list->poly[0]->vlist->n;
+ poly=1;
+ }
+ }
fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
- fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n, blist->n);
+ fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno, blist->n+monono*polyno);
fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
for(i=0;i<vlist->n;i++){
- fprintf(fh,"%u ",vlist->vertex[i].idx);
+ fprintf(fh,"%u ",vtx[i]->idx);
}
+ //polymeres
+ if(poly){
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ fprintf(fh,"%u ", vesicle->poly_list->poly[i]->vlist->vtx[j]->idx);
+ }
+ }
+ }
fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
for(i=0;i<vlist->n;i++){
- fprintf(fh,"%e %e %e\n",vtx[i].x,vtx[i].y, vtx[i].z);
+ fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
+ }
+ //polymeres
+ if(poly){
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
+ }
+ }
}
fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
for(i=0;i<blist->n;i++){
- fprintf(fh,"%u %u\n",blist->bond[i].vtx1->idx,blist->bond[i].vtx2->idx);
+ fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
}
+ //polymeres
+ if(poly){
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
+ fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx);
+ }
+ //grafted bonds
+ fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx);
+ }
+
+ }
+
+
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
- for (i=2;i<blist->n*2+1;i+=2){
+ for (i=2;i<(blist->n+monono*polyno)*2+1;i+=2){
fprintf(fh,"%u ",i);
}
fprintf(fh,"\n");
fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
- for (i=0;i<blist->n;i++){
+ for (i=0;i<blist->n+monono*polyno;i++){
fprintf(fh,"3 ");
}
@@ -240,10 +613,10 @@
}
ts_bool write_vertex_vtk_file(ts_vesicle *vesicle,ts_char *filename, ts_char *text){
- ts_vertex_list *vlist=&vesicle->vlist;
- ts_bond_list *blist=&vesicle->blist;
- ts_vertex *vtx=vlist->vertex;
- ts_uint i,j;
+ ts_vertex_list *vlist=vesicle->vlist;
+ ts_bond_list *blist=vesicle->blist;
+ ts_vertex **vtx=vlist->vtx;
+ ts_uint i;
FILE *fh;
fh=fopen(filename, "w");
@@ -260,12 +633,12 @@
fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
fprintf(fh,"POINTS %u double\n", vlist->n);
for(i=0;i<vlist->n;i++){
- fprintf(fh,"%e %e %e\n",vtx[i].x,vtx[i].y, vtx[i].z);
+ fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
}
fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
for(i=0;i<blist->n;i++){
- fprintf(fh,"2 %u %u\n",blist->bond[i].vtx1->idx,blist->bond[i].vtx2->idx);
+ fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
}
fprintf(fh,"CELL_TYPES %u\n",blist->n);
for(i=0;i<blist->n;i++)
@@ -276,7 +649,7 @@
fprintf(fh,"LOOKUP_TABLE default\n");
for(i=0;i<vlist->n;i++)
- fprintf(fh,"%u\n",vtx[i].idx);
+ fprintf(fh,"%u\n",vtx[i]->idx);
fclose(fh);
return TS_SUCCESS;
@@ -284,42 +657,119 @@
-ts_bool parsetape(ts_vesicle *vesicle,ts_uint *iterations){
- long int nshell=17,ncxmax=60, ncymax=60, nczmax=60; // THIS IS DUE TO CONFUSE BUG!
- ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
- *iterations=1000;
+ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){
+ long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20; // THIS IS DUE TO CONFUSE BUG!
+ char *buf=malloc(255*sizeof(char));
+ long int brezveze0=1;
+ long int brezveze1=1;
+ long int brezveze2=1;
+ ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0;
+ long int iter=1000, init=1000, mcsw=1000;
+
+
cfg_opt_t opts[] = {
CFG_SIMPLE_INT("nshell", &nshell),
+ CFG_SIMPLE_INT("npoly", &npoly),
+ CFG_SIMPLE_INT("nmono", &nmono),
CFG_SIMPLE_FLOAT("dmax", &dmax),
CFG_SIMPLE_FLOAT("xk0",&xk0),
+ CFG_SIMPLE_FLOAT("k_spring",&kspring),
CFG_SIMPLE_FLOAT("stepsize",&stepsize),
CFG_SIMPLE_INT("nxmax", &ncxmax),
CFG_SIMPLE_INT("nymax", &ncymax),
CFG_SIMPLE_INT("nzmax", &nczmax),
- CFG_SIMPLE_INT("iterations",iterations),
+ CFG_SIMPLE_INT("iterations",&iter),
+ CFG_SIMPLE_INT("mcsweeps",&mcsw),
+ CFG_SIMPLE_INT("inititer", &init),
CFG_SIMPLE_BOOL("quiet",&quiet),
+ CFG_SIMPLE_STR("multiprocessing",buf),
+ CFG_SIMPLE_INT("smp_cores",&brezveze0),
+ CFG_SIMPLE_INT("cluster_nodes",&brezveze1),
+ CFG_SIMPLE_INT("distributed_processes",&brezveze2),
CFG_END()
};
cfg_t *cfg;
ts_uint retval;
cfg = cfg_init(opts, 0);
- retval=cfg_parse(cfg, "tape_new");
+ retval=cfg_parse(cfg, "tape");
if(retval==CFG_FILE_ERROR){
- fatal("No tape_new file.",100);
+ fatal("No tape file.",100);
}
else if(retval==CFG_PARSE_ERROR){
fatal("Invalid tape!",100);
}
+ ts_vesicle *vesicle;
+ *iterations=iter;
+ *inititer=init;
+ *mcsweeps=mcsw;
+ vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
+ vesicle->poly_list=init_poly_list(npoly,nmono, vesicle->vlist);
+ vesicle->spring_constant=kspring;
+ poly_assign_spring_const(vesicle);
+
+
vesicle->nshell=nshell;
vesicle->dmax=dmax*dmax;
vesicle->bending_rigidity=xk0;
vesicle->stepsize=stepsize;
- vesicle->clist.ncmax[0]=ncxmax;
- vesicle->clist.ncmax[1]=ncymax;
- vesicle->clist.ncmax[2]=nczmax;
- vesicle->clist.max_occupancy=8;
- cfg_free(cfg);
-// fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
- return TS_SUCCESS;
+ vesicle->clist->ncmax[0]=ncxmax;
+ vesicle->clist->ncmax[1]=ncymax;
+ vesicle->clist->ncmax[2]=nczmax;
+ vesicle->clist->max_occupancy=8;
+ cfg_free(cfg);
+ free(buf);
+ // fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
+
+
+
+ return vesicle;
+
+}
+
+
+ts_bool read_geometry_file(char *fname, ts_vesicle *vesicle){
+ FILE *fh;
+ ts_uint i, nvtx,nedges,ntria;
+ ts_uint vtxi1,vtxi2;
+ float x,y,z;
+ ts_vertex_list *vlist;
+ fh=fopen(fname, "r");
+ if(fh==NULL){
+ err("Cannot open file for reading... Nonexistant file?");
+ return TS_FAIL;
+ }
+ ts_uint retval;
+ retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
+ vesicle->vlist=init_vertex_list(nvtx);
+ vlist=vesicle->vlist;
+ for(i=0;i<nvtx;i++){
+ // fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
+ retval=fscanf(fh,"%F %F %F",&x,&y,&z);
+ vlist->vtx[i]->x=x;
+ vlist->vtx[i]->y=y;
+ vlist->vtx[i]->z=z;
+ }
+ for(i=0;i<nedges;i++){
+ retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
+ bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
+ }
+ //TODO: neighbours from bonds,
+ //TODO: triangles from neigbours
+
+// Don't need to read triangles. Already have enough data
+ /*
+ for(i=0;i<ntria;i++){
+ retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
+ vtxi1=vesicle->blist->vertex1->idx;
+ vtxi2=vesicle->blist->vertex1->idx;
+
+ }
+ */
+ if(retval);
+ fclose(fh);
+
+
+
+ return TS_SUCCESS;
}
--
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